RetrogeneDB ID: retro_oglu_6

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 6:6067477..6068977(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM06G07920
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM05G25120
• Aliases: None
• Description: None

Sequence

>retro_oglu_6
ATGGCGGCGGCGGCGGTGGCGGCAGATCAGAAGGTGGTGACGATGACGAGCCTCCGGGAGGGCTGCGCTTGCGCGGCGCC
TCCTGCTGCATCTGCGCCGCCGGTGCCGAAGATGGCGGCGGCGCAGAGGGTGGTGGCGGAGCTGAGAGAGGCGTGCGCGA
CGCCGGCGGCGAGGCTGGCGGAGGTGGCCGCGGCGATGGCCGGCGAGATGGAGGCCGGGCTGGCGGTGGAGGGCGGCAGC
AGCGAGATGAAGATGATCGTGTCGTACGTCGACAGCCTCCCCACCGGCGGCGAGGAGGGGTCGTTCTACGCGCTCGACCT
CGGCGGCACCAACTTCCGCGTCCTCCGCGTGCGGCTCGCCGGCGGCGGCGTCGCCGAGCGCGTGGCGAGGGAGGTCCCGA
TCCCTTCCGGCCTCATGTCCGGCGGCGGCGCCACCTCGGAGCGCCTCTTCGGTTTCATCGCCTCCGCGCTGGCCGAGTTC
GTCGGCGAGGAGGAGGAAGAAGGCGGCCTCGACGGCGGCGAGAGGGAGCTTGGGTTCACCTTCTCCTTCCCCGTGCACCA
GACGTCCATCGCGTCCGGGACGCTCATCCGGTGGACGAAGGCGTTCGCCGTCGACGACGCAATCGGCGAGGACGTCGTGG
CGGCGCTGCAGGCGGCCATGTCGGAGCGGGGGCTCGACATGCGCGTGTCGGCGCTCATCAACGACACCGTCGGGACGCTC
GCCGCGGGCAGCTACTACGACGAGGACGTCGTGGCCGCCGTCATCCTCGGCACCGGCACGAACGCCGCCTACGTCGAGGA
CGCCACCGCCATCGCCAAGCTACACCCATCGCAGCTGCCAGCATCGAACACCATGGTGATCAACACCGAGTGGGGCAGCT
TCGCCTCGCCGTGCCTCCCATTGACGGAGTTCGACGAAGCGCTCGATCAGGAGAGCCTCAACCCCGGCGAGCAAACCTAC
GAGAAGCTCATCTCCGGGATGTACCTCGGCGAGATCGTCAGGAGGGTCCTCCTCAAGGTCTCCTCCCGGTGCCCCTCCCT
CCTCGGCGGCGCCGGCGAGCTCGCGACGCCGTTCGTCCTCAGGACACCCGACGTGTCCGCGATGCACCACGACGAGACGC
CCGAGCTGAGCATCGTCGGCGAGAAGCTGGAACGCACGCTGGGCATCCGCGGCACGTCGCCGGAGGCGAGGAGGATGGTC
GTCGAGGTGTGCGACATCGTGGCCACGAGGGCCGCCCGGCTGGCCGCGGCGGGGATCGTCGGGATCCTGAAGAAGATCGG
GAGGGTCGACGGCGGCGAGGGGCGGAGAAGGAGGTCGGTGGTCGCCGTCGACGGCGGGCTGTTCGAGCACTACGGCAAGT
TCCGGCGGTGCATGGAGAGCGCGGTGAGGGAGATGCTCGGAGAGGAGGCGGCGGCGGAGAGGGTGGTCGTCAAGCTCGCC
AGCGACGGCTCCGGGCTCGGCGCCGCCCTGGTTGCAGCTGCTCACTCGCAGAGAGCATAA

Alignment

ORF - retro_oglu_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.2 %
• Parental protein coverage: 91.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADAVLRELEERCAAPPARLRQVADAMAVEMHAGLASEGGS-KLKMIISYVDALPSGEEKGVFYALDLGGT
          A..V..EL.E.CA.P.ARL..VA.AMA.EM.AGLA.EGGS...KMI.SYVD.LP.G.E.G.FYALDLGGT
Retrocopy AQRVVAELREACATPAARLAEVAAAMAGEMEAGLAVEGGSSEMKMIVSYVDSLPTGGEEGSFYALDLGGT

Parental  NFRVLRVQLGGKEGRVIKQEHDEISIPPHLMTGG---SNELFDFIASSLAKFVASEGEDFHLAEGRQREL
          NFRVLRV.L.G..G.V......E..IP..LM.GG...S..LF.FIAS.LA.FV..E.E...L..G..REL
Retrocopy NFRVLRVRLAG--GGVAERVAREVPIPSGLMSGGGATSERLFGFIASALAEFVGEEEEEGGL-DGGEREL

Parental  GFTFSFPVKQTSIASGTLINWTKGFSIDETVGEDVVTELTKALERQGLDMKVTALINDTIGTLAGGRYDD
          GFTFSFPV.QTSIASGTLI.WTK.F..D...GEDVV..L..A....GLDM.V.ALINDT.GTLA.G.Y.D
Retrocopy GFTFSFPVHQTSIASGTLIRWTKAFAVDDAIGEDVVAALQAAMSERGLDMRVSALINDTVGTLAAGSYYD

Parental  NDVIAAVILGTGTNAAYVERANAIPKWH-DLLPKSGDMVINMEWGNFRSSHLPLTEFDQALDAESLNPGE
          .DV.AAVILGTGTNAAYVE.A.AI.K.H...LP.S..MVIN.EWG.F.S..LPLTEFD.ALD.ESLNPGE
Retrocopy EDVVAAVILGTGTNAAYVEDATAIAKLHPSQLPASNTMVINTEWGSFASPCLPLTEFDEALDQESLNPGE

Parental  QVYEKLISGMYLGEIVRRVLLKMAEEA-SLFGDEVPPKLKIPFIIRTPYMSMMHCDRSPDLRTVGAKLKD
          Q.YEKLISGMYLGEIVRRVLLK......SL.G......L..PF..RTP..S.MH.D..P.L..VG.KL..
Retrocopy QTYEKLISGMYLGEIVRRVLLKVSSRCPSLLGG--AGELATPFVLRTPDVSAMHHDETPELSIVGEKLER

Parental  ILGVQSTSLKTRRLVVDVCDIVAKRAACLAAAGIHGILKKLGR-DVPNTDKQRTVIAVDGGLYEHYTIFA
          .LG...TS...RR.VV.VCDIVA.RAA.LAAAGI.GILKK.GR.D.......R.V.AVDGGL.EHY..F.
Retrocopy TLGIRGTSPEARRMVVEVCDIVATRAARLAAAGIVGILKKIGRVDGGEGRRRRSVVAVDGGLFEHYGKFR

Parental  ECVESTLRDMLGEEVSS-TIVIKLAKDGSGIGAALLAAAHSQ
          .C.ES..R.MLGEE......V.KLA.DGSG.GAAL.AAAHSQ
Retrocopy RCMESAVREMLGEEAAAERVVVKLASDGSGLGAALVAAAHSQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza glumaepatula was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza glumaepatula was not studied using ChIP-Seq data.

EST

Oryza glumaepatula was not studied using EST data.

TSS

Oryza glumaepatula was not studied using FANTOM5 data.

Lab

retro_oglu_6 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glumaepatula does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA017675	1 retrocopy	retro_oind_38,
Oryza barthii	OBART05G23750	1 retrocopy	retro_obar_3,
Oryza glumaepatula	OGLUM05G25120	1 retrocopy	retro_oglu_6 ,
Oryza nivara	ONIVA05G24490	1 retrocopy	retro_oniv_15,
Oryza rufipogon	ORUFI05G25500	1 retrocopy	retro_oruf_35,